1k Genomes

1kG: HG01440
MDKA Birth: Colombia

Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z272 > S450 > Z295/S1217 > ZZ77 > Z216 > S452 > ~19966372-C-T > Exact position not yet finalized.

Unique Mutations

The mutations unique to this man are summarized in the table below. Those with a '+' or '*' confidence level are considered by FamilyTreeDNA or FullGenomesCorp to be high quality SNPs/INDELs. For completeness, all other mutations of lesser confidence are included as well. These additional mutations may be useful for distinguishing between very closely related men.

Occasionally, some of the mutations listed here will be thought to be shared with other men in which case they might appear in upstream blocks on the tree. When this happens, the 'Blocks' field will indicate what block they appear in. Such a situation might arise with BigY men if the BED data suggests another man may be positive for a SNP, even though it doesn't appear in his VCF data. It might also happen if Chromo2 testing or Sanger sequencing of other men not on the tree show the SNP to be shared.

POS-REF-ALT (hg19) POS-REF-ALT (hg38) Blocks Names Region McDonald BED combBED STR1kG
HG01440		Manual
Edits
6006782-A-G 6138741-A-G ZS203 +
13707106-T-A 11551430-T-A +
5905918-G-A 6037877-G-A FT166836 +
3580631-C-G 3712590-C-G +
13306490-A-G 11150814-A-G +
17479396-C-A 15367516-C-A YY13×A+
2716832-G-C 2848791-G-C BY55978 YY+
6900054-G-T 7032013-G-T FT167183 YY+
7425453-C-T 7557412-C-T F15887 YY+
8124607-C-T 8256566-C-T FT300341 YY+
8307359-A-C 8439318-A-C BY71569 YY+
8337827-C-T 8469786-C-T PF287 YY+
8463626-G-A 8595585-G-A Y86948 ALK223 YY+
8539157-C-A 8671116-C-A FT300471 YY+
8848420-C-G 8980379-C-G FT300552 YY+
9009431-G-T 9171822-G-T FT300596 Y+
14615090-C-A 12503288-C-A CTS3008 Y+
15855303-G-T 13743423-G-T CTS4834 Y+
16256736-G-T 14144856-G-T Y29514 YY9×T+
16499694-C-T 14387814-C-T CTS5836 Y+
16833967-C-A 14722087-C-A CTS6339 YY+
17001903-T-C 14890023-T-C CTS6602 Y+
17099268-A-G 14987388-A-G CTS6768 YY+
17251305-A-G 15139425-A-G CTS7036 YY+
17656630-C-T 15544750-C-T CTS7774 YY+
18628130-A-C 16516250-A-C CTS9037 YY+
19396589-A-C 17284709-A-C CTS10322 YY+
21257640-C-G 19095754-C-G FT302275 YY+
21685311-T-A 19523425-T-A BY134715 YY+
22164428-G-T 20002542-G-T FT302599 YY+
22556553-C-T 20394667-C-T BY138981 YY+
22591965-C-A 20430079-C-A FT302655 YY+
22602467-G-A 20440581-G-A FT112180 YY+
22845012-T-TA 20683126-T-TA 10×A+
22992068-T-G 20830182-T-G BY142195 YY+
13504062-A-G 11348386-A-G +
2651902-TG-T 2783861-TG-T +
2954157-C-T 3086116-C-T FT315539 +
3357173-T-C 3489132-T-C +
3445932-G-A 3577891-G-A FT317273 +
3469884-T-A 3601843-T-A +
3509911-T-C 3641870-T-C +
3543119-A-G 3675078-A-G FT317630 +
3548687-T-TTTTG 3680646-T-TTTTG +
3583549-A-G 3715508-A-G S8595 +
3736774-C-T 3868733-C-T +
3899405-G-C 4031364-G-C +
4067369-T-A 4199328-T-A 26×A+
4221228-GTA-G 4353187-GTA-G +
4679054-C-T 4811013-C-T FT82877 +
4779537-G-A 4911496-G-A +
4792876-A-C 4924835-A-C +
4876788-G-T 5008747-G-T +
5344234-T-G 5476193-T-G +
5842372-A-G 5974331-A-G +
6089907-TA-T 6221866-TA-T +
6121168-G-A 6253127-G-A +
6402301-A-C 6534260-A-C +
6580438-T-G 6712397-T-G +
7103104-C-A 7235063-C-A YY+
7195306-GC-G 7327265-GC-G +
8706660-C-T 8838619-C-T YY+
9885644-CA-C 10048035-CA-C +
9885646-AC-A 10048037-AC-A +
9964276-G-T 10126667-G-T Y+
10054205-G-T 10216596-G-T +
13222660-G-T 11066984-G-T +
13265088-C-T 11109412-C-T +
13295304-AG-A 11139628-AG-A +
13305060-C-G 11149384-C-G +
13308862-T-C 11153186-T-C F10660 +
13308863-G-A 11153187-G-A +
13309001-A-G 11153325-A-G +
13389651-GTATATA-G 11233975-GTATATA-G 8×TA+
13433185-C-T 11277509-C-T +
13447260-T-TCCAC 11291584-T-TCCAC +
13447261-T-TCATTC 11291585-T-TCATTC +
13447268-A-ACTCCC 11291592-A-ACTCCC +
13510595-C-T 11354919-C-T +
13806014-G-A 11685308-G-A BY15215 +
13908794-G-T 11788088-G-T Y+
14833439-A-C 12721506-A-C CTS3324 YY+
15216997-T-G 13105083-T-G CTS3834 Y+
15305459-A-G 13193558-A-G YY+
15398457-T-G 13286577-T-G Z13387 Y+
15532559-C-T 13420679-C-T M4991 YY+
15876381-AT-A 13764501-AT-A +
15928797-A-C 13816917-A-C CTS4964 YY+
15954956-T-C 13843076-T-C FT301293 YY+
16027139-T-G 13915259-T-G Y+
16345190-TTTC-T 14233310-TTTC-T +
17126567-A-C 15014687-A-C Y+
17153148-C-A 15041268-C-A YY+
17163965-G-T 15052085-G-T CTS6875 Y+
18172299-C-A 16060419-C-A YY+
18556553-GCT-G 16444673-GCT-G +
18863053-T-G 16751173-T-G Y+
18868080-T-A 16756200-T-A CTS9386 YY+
19520844-TTA-T 17408964-TTA-T +
20842572-AAG-A 18680686-AAG-A P4_Dst +
22235481-C-T 20073595-C-T DYZ19 +
22289308-A-G 20127422-A-G DYZ19 +
22294753-G-C 20132867-G-C DYZ19 +
22459047-A-C 20297161-A-C DYZ19 +
22474382-G-T 20312496-G-T BY48632 DYZ19 +
22981817-AG-A 20819931-AG-A +
23157802-G-T 20995916-G-T FGC6806Y2662 FGC6803 Y+
23994430-C-T 21848283-C-T Y1129 +
27454634-G-A 25308487-G-A P1_Y2 +
58895590-C-T 56695281-G-A +
58895649-C-A 56695222-G-T +

In the table above, the meaning of the confidence field depends on whether the data comes from an FTDNA kit or an FGC kit. For FTDNA kits, + implies a "PASS" result with just one possible variant, * indicates a "PASS" but with multiple variants, ** indicates "REJECTED" with just a single variant, and *** indicates "REJECTED" with multiple possible variants. 'A*' are heterozygous variants not called by FTDNA, but still pulled from the VCF file. For FGC kits, + indicates over 99% likely genuine (95% for INDELs); * over 95% likely genuine (90% for INDELs); ** about 40% likely genuine; *** about 10% likely genuine. Manual entries read directly from a BAM file will be either + indicating positive, or * indicating that the data show a mixture of possible variants.

For the FTDNA kits, the BED data is encoded in the background color of the cells. Those cells with a white background have coverage, those with a grey background indicate no coverage in the BED file, and those with a pink background indicate the mutation is on the edge of a coverage region. These pink regions often indicate that the individual may be positive for a SNP even if there is no corresponding entry in the vcf file.

The combBED column indicates whether or not the mutation is a SNP and falls in the combBED region defined in Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data by Dmitry Adamov, Vladimir Guryanov, Sergey Karzhavin, Vladimir Tagankin, Vadim Urasin.

The McDonald BED column indicates whether or not the mutation is a SNP and falls in the BED region used by Dr. Iain McDonald in the age analysis he does for R-U106 men.

Mutation Notes:

Kit POSITION-REF-ALT (hg19) POSITION-REF-ALT (hg38) Note
Manual19966372-C-T17854492-C-T1C 4T
Manual22248660-G-T20086774-G-T1G 2T